OR1D2
protein-codingolfactory receptor family 1 subfamily D member 2, the group of Olfactory receptors, family 1
Gene summary
Olfactory receptors interact with odorant molecules in the nose, to initiate a neuronal response that triggers the perception of a smell. The olfactory receptor proteins are members of a large family of G-protein-coupled receptors (GPCR) arising from single coding-exon genes. Olfactory receptors share a 7-transmembrane domain structure with many neurotransmitter and hormone receptors and are responsible for the recognition and G protein-mediated transduction of odorant signals. The olfactory receptor gene family is the largest in the genome. [provided by RefSeq, Jul 2008]
- OLFR1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~15.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to OR1D2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002548.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 32 | 2 | 34 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 32 | 2 | 0 | 34 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002539.2 | 1 | MANE Select | |
| Ensembl | ENSP00000493103.1 | 1 | MANE Select | |
| RefSeq | NP_001373017.1 | 1 | Standard | |
| Ensembl | ENSP00000493077.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Olfactory transduction - Homo sapiens (human)
- Olfactory receptor activity
- GPCRs, Class A Rhodopsin-like
- Signaling by GPCR
- Signal Transduction
Biological Process
- chemotaxis
- G protein-coupled receptor signaling pathway
- single fertilization
- sensory perception of smell
- detection of chemical stimulus involved in sensory perception of smell
Molecular Function
- G protein-coupled receptor activity
- olfactory receptor activity
- identical protein binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000331459
- Coding exons
- 1
- Length
- 939
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0736 | 159 | 162 | 0.984 | 0.00000795 | 2031 |
| Missense (PolyPhen) | 37 | 46.069 | 0.80314 | 669 | ||
| Synonymous | -0.0314 | 69 | 68.7 | 1.00 | 0.00000337 | 662 |
| Loss of Function | 0.488 | 5 | 6.33 | 0.790 | 3.69e-7 | 86 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Odorant receptor which may be involved in sperm chemotaxis. Bourgeonal is a strong chemoattractant for sperm in vitro and is shown to be a strong agonist for OR1D2 in vitro. May also function in olfactory reception. {ECO:0000269|PubMed:12663925, ECO:0000269|PubMed:15458659, ECO:0000269|PubMed:16820410}.;
Recessive Scores
- pRec
- 0.0871
Intolerance Scores
- LoFtool
- 0.711
- RVIS EVS
- 1.02
- RVIS percentile EVS
- 90.92
Essentials
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0638
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |